There are several themes present inside Atlas Shrugged. Here are the ones I picked up on.

The Evils of Collectivism: You couldn't possibly think I'd miss this one could you? All through the novel, Ayn Rand harps constantly upon the necrosis caused by communist and socialist governments. When men, through collectivism, are forced to put others ahead of themselves, supporting others while they themselves wither, incentive becomes destroyed and the only product is chaos and evil. The in novel "Twentieth Century Motor Company" is the best example of this. One of the workers from there tells Dagny of how the new owners of the plant had everyone vote on a new payment plan. They all decided that everyone would be worked according to his ability and paid according to his need. The plant quickly failed and the town surrounding it was destroyed by greed and mistrust.

SPOILERS!!!!!

The Importance of the Mind: This is the other main theme of the novel. By stopping the 'motor of the world', John Galt leads a strike of the mind. Society quickly degrades as Galt withdraws the best and most creative minds available. As society denies logic as a phallacy and ignores the need for those who produce, humanity's debt to those who think is clear. As the events of the novel show, the mind enables creation and innovation and powers the engine of the world. Labor alone cannot achieve productivity and prosperity without the guidance of the mind.